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- PDB-2pie: Crystal structure of the FHA domain of RNF8 in complex with its o... -

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Basic information

Entry
Database: PDB / ID: 2pie
TitleCrystal structure of the FHA domain of RNF8 in complex with its optimal phosphopeptide
Components
  • E3 ubiquitin-protein ligase RNF8
  • phosphopeptide
KeywordsLIGASE / FHA domain / phosphopeptide / complex / SIGNALING PROTEIN
Function / homology
Function and homology information


sperm DNA condensation / protein K6-linked ubiquitination / isotype switching / DNA repair-dependent chromatin remodeling / response to ionizing radiation / cell division site / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / signal transduction in response to DNA damage ...sperm DNA condensation / protein K6-linked ubiquitination / isotype switching / DNA repair-dependent chromatin remodeling / response to ionizing radiation / cell division site / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / signal transduction in response to DNA damage / protein autoubiquitination / protein K48-linked ubiquitination / interstrand cross-link repair / epigenetic regulation of gene expression / ubiquitin ligase complex / positive regulation of DNA repair / ubiquitin binding / Nonhomologous End-Joining (NHEJ) / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / double-strand break repair via nonhomologous end joining / ubiquitin protein ligase activity / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / midbody / histone binding / ubiquitin-dependent protein catabolic process / chromosome, telomeric region / cell cycle / cell division / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF8 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / Zinc finger, RING-type, conserved site ...E3 ubiquitin-protein ligase RNF8 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGrant, R.A. / Yaffe, M.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: RNF8 Transduces the DNA-Damage Signal via Histone Ubiquitylation and Checkpoint Protein Assembly.
Authors: Huen, M.S. / Grant, R. / Manke, I. / Minn, K. / Yu, X. / Yaffe, M.B. / Chen, J.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF8
F: phosphopeptide


Theoretical massNumber of molelcules
Total (without water)16,8122
Polymers16,8122
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.632, 76.865, 120.744
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein E3 ubiquitin-protein ligase RNF8 / RING finger protein 8


Mass: 15791.998 Da / Num. of mol.: 1 / Fragment: N terminal FHA domain of RNF8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF8, KIAA0646 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2
References: UniProt: O76064, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide phosphopeptide


Mass: 1020.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic phosphopeptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 277 K / Method: batch crystallization / pH: 8
Details: 4 mM Tris pH 8, 4 mM NaCl, 0.4 mM DTT, pH 8.0, batch crystallization, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979462 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2006
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979462 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 35871 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.067 / Χ2: 1.719 / Net I/σ(I): 12.2
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.354 / Num. unique all: 3534 / Χ2: 0.507 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4.5 Å31.55 Å
Translation4.5 Å31.55 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CSW

2csw


Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.507 / SU ML: 0.032 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1812 5.1 %RANDOM
Rwork0.181 ---
obs0.182 35808 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 190 1429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221282
X-RAY DIFFRACTIONr_bond_other_d0.0020.02891
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9621757
X-RAY DIFFRACTIONr_angle_other_deg0.90832173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27923.65163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62415230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2891511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021463
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
X-RAY DIFFRACTIONr_nbd_refined0.1970.2182
X-RAY DIFFRACTIONr_nbd_other0.1920.2878
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2591
X-RAY DIFFRACTIONr_nbtor_other0.0830.2711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4270.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4030.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.217
X-RAY DIFFRACTIONr_mcbond_it1.1771.51000
X-RAY DIFFRACTIONr_mcbond_other0.2261.5309
X-RAY DIFFRACTIONr_mcangle_it1.32221236
X-RAY DIFFRACTIONr_scbond_it2.0373630
X-RAY DIFFRACTIONr_scangle_it2.8354.5512
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 126 -
Rwork0.202 2435 -
obs-2561 97.9 %

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